rs3754112
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001256106.3(CD101):āc.674A>Gā(p.Asn225Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 1,613,850 control chromosomes in the GnomAD database, including 71,147 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001256106.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD101 | NM_001256106.3 | c.674A>G | p.Asn225Ser | missense_variant | 3/10 | ENST00000682167.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD101 | ENST00000682167.1 | c.674A>G | p.Asn225Ser | missense_variant | 3/10 | NM_001256106.3 | P1 | ||
CD101 | ENST00000369470.1 | c.674A>G | p.Asn225Ser | missense_variant | 3/10 | 1 | P1 | ||
CD101 | ENST00000256652.8 | c.674A>G | p.Asn225Ser | missense_variant | 3/9 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.230 AC: 35033AN: 152012Hom.: 4988 Cov.: 32
GnomAD3 exomes AF: 0.249 AC: 62534AN: 250790Hom.: 9060 AF XY: 0.255 AC XY: 34510AN XY: 135528
GnomAD4 exome AF: 0.293 AC: 427730AN: 1461720Hom.: 66159 Cov.: 39 AF XY: 0.291 AC XY: 211668AN XY: 727156
GnomAD4 genome AF: 0.230 AC: 35020AN: 152130Hom.: 4988 Cov.: 32 AF XY: 0.226 AC XY: 16790AN XY: 74380
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 23, 2021 | This variant is associated with the following publications: (PMID: 29108000) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at